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1,000 results • Page
3 of 20
Sort: Views
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Views
Votes
Replies
6
votes
8
replies
10k
views
7 follow
Converting SNP names from Illumina GSA array to rsID using PLINK
SNP
plink
6.5 years ago by
dam4l
▴ 200
4
votes
6
replies
10.0k
views
Spades assembler output
Assembly
updated 21 months ago by
Ram
43k • written 8.3 years ago by
elbecerrasoto
▴ 30
0
votes
8
replies
9.9k
views
how to find a read by name in a bam file
next-gen-sequencing
updated 10 months ago by
Ram
43k • written 6.8 years ago by
himanimalhotra89
• 0
3
votes
10
replies
9.9k
views
How can I obtain SNP from TCGA?
Risky-allele
BRCA
SNP
updated 2.3 years ago by
Ram
43k • written 9.6 years ago by
purmod
▴ 10
3
votes
5
replies
9.9k
views
pheatmap: how to avoid fontface, fontsize, and color from writing over existing rownames
fontsize
rows
color
R
pheatmap
updated 2.9 years ago by
cpad0112
21k • written 2.9 years ago by
ladypurrsia
▴ 60
0
votes
2
replies
9.8k
views
DESeq2 pheatmap returns Error in check.length("fill") : 'gpar' element 'fill' must not be length 0
RNA-Seq
DESeq2
gpar
pheatmap
6.5 years ago by
Anthony.Knox
▴ 60
0
votes
4
replies
9.8k
views
How to install PLINK on linux/Mac-OS
genome
3.5 years ago by
giusdalt95
▴ 10
11
votes
29
replies
9.8k
views
SummarizedExperiment nrow differs from ncol
DESeq2
SummarizedExperiment
updated 2.5 years ago by
Ram
43k • written 9.9 years ago by
Parham
★ 1.6k
2
votes
2
replies
9.8k
views
Multiple whole genome alignment tools ?
multiple whole genome
alignment
4.9 years ago by
Picasa
▴ 640
4
votes
10
replies
9.7k
views
Questions about multithreading of BWA
bwa
multithread
updated 5.6 years ago by
Ram
43k • written 8.2 years ago by
michealsmith
▴ 790
1
vote
4
replies
9.7k
views
R ggplot Align Y-Axis on multiple graphs
ggarrange
ggplot2
r
updated 4.7 years ago by
Biostar
20 • written 6.2 years ago by
jjrin
▴ 40
1
vote
13
replies
9.7k
views
MDS Plot R
RNA-Seq
4.8 years ago by
BioBaby
▴ 20
4
votes
3
replies
9.6k
views
Convert Tab delimited file to VCF file
snp
updated 23 months ago by
Ram
43k • written 8.5 years ago by
niharraul
• 0
2
votes
17
replies
9.6k
views
7 follow
EXITING: because of fatal INPUT file error: could not open read file
mapping
genome
fastq
STAR
updated 2.1 years ago by
todd.ugine
• 0 • written 3.3 years ago by
merfer0206
• 0
1
vote
6
replies
9.6k
views
How to use python to process .CEL file?
cel
affymetrix
python
R
cmap
updated 23 months ago by
Ram
43k • written 9.1 years ago by
zero_hsy
▴ 110
5
votes
11
replies
9.5k
views
R- Kruskal-Wallis test on multiple columns at once
R
statistics
test
kruskal-Wallis
R-statistics
4.7 years ago by
mafernandez
• 0
0
votes
19
replies
9.5k
views
Skip orientation as there are not enough pairs by bwa mem
whole genome
bwa
paired end sequencing
4.9 years ago by
seta
★ 1.9k
3
votes
8
replies
9.5k
views
topTable in limma
limma
toptable
6.5 years ago by
AHW
▴ 90
3
votes
9
replies
9.5k
views
Random Forest returns "New factor levels not present in the training data"
R
Machine Learning
microarrays
6.2 years ago by
arronar
▴ 280
1
vote
6
replies
9.5k
views
Deseq2 : Filtering low counts before per sample
Deseq2
threshold-seq
5.4 years ago by
Cdk
• 0
3
votes
5
replies
9.5k
views
Using 'blastn' to do a remote search on NCBI BLAST against the nt collection database
blast
shell
unix
linux
6.2 years ago by
maciwuk
• 0
3
votes
7
replies
9.5k
views
6 follow
remote blast requires installation of taxdb database
blast
updated 4.9 years ago by
Varshney
▴ 20 • written 6.5 years ago by
hfan22
▴ 40
2
votes
2
replies
9.5k
views
Imputation Analysis In Plink?
plink
gwas
imputation
12.2 years ago by
Davy
▴ 210
7
votes
5
replies
9.5k
views
strange issues with absent EOF markers in BAM files
samtools
picard-tools
bam
eof
7.9 years ago by
abascalfederico
★ 1.2k
2
votes
12
replies
9.4k
views
8 follow
michigan imputation server
conversion
michigan imputation server
updated 2.4 years ago by
Fazil
• 0 • written 6.2 years ago by
Teresa
▴ 20
4
votes
2
replies
9.4k
views
Hisat2 versus Bowtie2
Exome-sequencing
hisat2
bowtie2
updated 6.8 years ago by
Biostar
20 • written 8.0 years ago by
nalpas.nicolas
▴ 20
2
votes
7
replies
9.4k
views
How to annotate TTS or TES
ChIP-Seq
TES
annotation
7.2 years ago by
Lila M
★ 1.2k
0
votes
11
replies
9.3k
views
Error in installation R package
R
updated 7.6 years ago by
Biostar
20 • written 7.7 years ago by
niutster
▴ 110
4
votes
8
replies
9.3k
views
Quantile normalizing prior to or after TPM scaling?
RNAseq
normalization
updated 14 months ago by
Kevin Blighe
87k • written 6.4 years ago by
mforde84
★ 1.4k
5
votes
12
replies
9.3k
views
ADMIXTURE: "Invalid chromosome code. Use integers!"
admixture
genome
7.2 years ago by
beneficii
▴ 60
7
votes
8
replies
9.3k
views
Removing rRNA and tRNA sequences using GTF files
RNA-Seq
7.7 years ago by
pixie@bioinfo
★ 1.5k
4
votes
1
reply
9.2k
views
Need help with heatmaps in R, how to draw select genes or selected pathway??
RNA-Seq
DESEQ2
R
heatmap
ontology
updated 7.6 years ago by
Biostar
20 • written 7.6 years ago by
marina.kimyr
▴ 20
3
votes
8
replies
9.2k
views
DiffBind: Error in `.rowNamesDF<-`(x, value = value) : invalid 'row.names' length
R
DiffBind
ChIP-Seq
5.1 years ago by
msimmer92
▴ 300
1
vote
2
replies
9.1k
views
Problem in merging 1000G and cases in Plink
merge
duplicate snp
plink
triallelic
1000G
7.6 years ago by
fatima
▴ 20
10
votes
11
replies
9.1k
views
How to adjust my manhattan plot to look better?
qqman
manhattan
R
updated 23 months ago by
Ram
43k • written 9.1 years ago by
SheelS
▴ 40
3
votes
10
replies
9.0k
views
How to remove outliers using PCA in R?
PCA
R
4.8 years ago by
zhaoliang0302
▴ 50
3
votes
4
replies
9.0k
views
how to filter vcf file based on sample DP? vcf tools does not work
vcf-filtering
sample DP
7.1 years ago by
Ana
▴ 200
3
votes
0
replies
9.0k
views
edgeR: how to make contrasts with makeContrasts
ngs
edgeR
makeContrasts
glm
dge
5.5 years ago by
m98
▴ 420
13
votes
13
replies
9.0k
views
How to do pca plot from .eigenval and .eigenvec files from Plink in R.
R
SNP
updated 6.1 years ago by
Devon Ryan
104k • written 6.1 years ago by
amitgourav.ghosh12
▴ 70
7
votes
8
replies
9.0k
views
Determining read count
trimmomatic
rna-seq
trinity
updated 8 months ago by
Ram
43k • written 8.0 years ago by
nikelle.petrillo
▴ 110
4
votes
9
replies
8.9k
views
bcftools consensus command
vcf
bcftools
updated 13 months ago by
Ram
43k • written 4.3 years ago by
Begonia_pavonina
▴ 150
3
votes
4
replies
8.9k
views
Design Pcr Primers To Uniquely Identify A Bacterial Strain
bacteria
pcr
updated 10.5 years ago by
Biostar
20 • written 10.5 years ago by
Eric Normandeau
11k
2
votes
3
replies
8.9k
views
what is the detailed information of .amb .ann .bwt .pac .sa files generated by the BWA aligner?
alignment
BWA
.ann
.bwt
.sa
updated 6.2 years ago by
WouterDeCoster
47k • written 6.2 years ago by
lffu_0032
▴ 90
5
votes
10
replies
8.9k
views
GWAS - approximate odds ratio and standard error
GWAS
imputation
updated 6.5 years ago by
Kevin Blighe
87k • written 6.5 years ago by
alessandrotestori7
▴ 420
2
votes
8
replies
8.8k
views
Questions: how to do GSEA for single cells?
RNA-Seq
3.9 years ago by
yingnanlei0202
▴ 20
1
vote
3
replies
8.8k
views
Htseq Count Finding No Feature
htseq
bacteria
gene-expression
11.1 years ago by
joaslucas
▴ 90
2
votes
2
replies
8.8k
views
Plot minor allele frequency distribution in R?
gwas
maf
R
7.9 years ago by
dam4l
▴ 200
0
votes
4
replies
8.8k
views
ITCN 1.6 ImageJ Plugin
software error
updated 6.5 years ago by
Biostar
20 • written 7.5 years ago by
verma
▴ 30
1
vote
2
replies
8.8k
views
Install Plink V1.07 on Mac
software error
7.7 years ago by
xaviera417
• 0
3
votes
13
replies
8.8k
views
Actually meaning of log2FoldChange, p-value & padj in DESeq2 results
RNA-Seq
DESeq2
differentially expressed genes
5.5 years ago by
hffqyd
▴ 10
1,000 results • Page
3 of 20
Recent Votes
discoSnp - reference-free finding of isolated SNPs from non assembled reads
Comment: Figures are disappeared from html report of SnpEff
Answer: Figures are disappeared from html report of SnpEff
Comment: How to trim transcripts using information from NCBI contamination screen report
Filtering rRNA contamination (indicated by GC content plots) from RNA-seq data
Filtering rRNA contamination (indicated by GC content plots) from RNA-seq data
A: What is the VEP Impact column?
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Recent Replies
Comment: Is it possible to get a list of representative genomes from a past RefSeq releas
by
GenoMax
141k
At this point you should email NCBI help desk and ask them this question. If you get an answer then please post it back in this thread.
Comment: Figures are disappeared from html report of SnpEff
by
Pierre Lindenbaum
161k
the javascript in your html is deprecated or your firefox is just tool old.
Comment: Why gatk VariantAnnotator required bam and coverage files
by
Pierre Lindenbaum
161k
> I would like to ask why they may require the bam file for this function? hum.. if you want to add the coverage, where do you think gatk …
Comment: Figures are disappeared from html report of SnpEff
by
analyst
▴ 30
By following above approach I got this ![enter image description here][1] [1]: /media/images/b47490eb-d4c4-4f39-a7b2-f5b7b6b8
Comment: Highest variable features in single cell data
by
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I apologize for the confusion. What I meant to say is that, for example, the Trbv17 gene appears among the variable genes. However, when I …
Answer: why renaming Idents in Seurat object doesn't work?
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I manage to find a workwround, but I don't understand what I did wrong here. my solution was to extract the cluster column as vector and…
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Hi, thanks for letting us know. In a recent software update, we introduced a problem with the written splice information in the cached …
Comment: Fetch table from clinvar database according to a list of rsid
by
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▴ 20
so which one should i prefer? i don't need the entire results i need the condition-Germline table only. (for eg:-from, https://www.ncbi.nlm…
Comment: To get p-values for the TPM
by
dsull
★ 5.8k
OK, not sure why your intention is to use RSEM p-values for, but at least tell us the commands you ran then otherwise how are we supposed t…
Comment: Fetch table from clinvar database according to a list of rsid
by
Pierre Lindenbaum
161k
> Don't forget to follow up on your threads. If an answer was helpful, you should upvote it; if the answer resolved your question, you shou…
Comment: different FeatureCounts output for the same data
by
sehriban.buyukkilic
▴ 10
Sure, I'll inquire about the version of Rsubread. I'll keep you posted if it works :) Thanks
Comment: different FeatureCounts output for the same data
by
sehriban.buyukkilic
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Yeah, let me show you my featureCounts result, it looks like this. It's too low. [1]: /media/images/eb8293fe-e6ae-4b02-92e2-0ba2075b
Comment: Adding CB tag to bam file
by
Pierre Lindenbaum
161k
samtools addreplacerg is for read groups. This is not what OP asked.
Comment: Adding CB tag to bam file
by
Maria
• 0
When I try ``` samtools addreplacerg -r "@CB\tID:$cell" -o $cell.bam $LINE``` the CB tag gets add to the header, but the tag in every line …
Answer: Figures are disappeared from html report of SnpEff
by
Pierre Lindenbaum
161k
the remote website providing the javascript or/and the images is down or you're now behind a proxy. Check the firefox console: https://fire…
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